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2022 August
A nanopore interface for higher bandwidth DNA computing
Karen Zhang
Yuan-Jyue Chen
Delaney Wilde
Kathryn Doroschak
Karin Strauss
Luis Ceze
Georg Seelig
Jeff Nivala
Nature Communications.
2022 July
Recording gene expression order in DNA by CRISPR addition of retron barcodes
Santa Bhattarai-Kline
Sierra K. Lear
Chloe B. Fishman
Santiago C. Lopez
Elana R. Lockshin
Max G. Schubert
Jeff Nivala
George M. Church
Seth L. & Shipman
Nature.
2022 May
Passively sensing SARS-CoV-2 RNA in public transit buses
Jason S Hoffman
Matthew Hirano
Nuttada Panpradist
Joseph Breda
Parker Ruth
Yuanyi Xu
Jonathan Lester
Bichlien H Nguyen
Luis Ceze
Shwetak N Patel
Science of the Total Environment.
2022 April
Doctoring Direct-to-Consumer Genetic Tests with DNA Spike-Ins
Peter Ney
Arkaprabha Bhattacharya
David Ward
Luis Ceze
Tadayoshi Kohno
Jeff Nivala
biorxiv.
Preprint
2022 January
Synthetic DNA applications in information technology
Linda C. Meiser
Bichlien H. Nguyen
Yuan-Jyue Chen
Jeff Nivala
Karin Strauss
Luis Ceze
Robert N. Grass
Nature Communications.
Review
2021 November
Scaling DNA data storage with nanoscale electrode wells
Bichlien H. Nguyen
Christopher N. Takahashi
Gagan Gupta
Jake A. Smith
Richard Rouse
Paul Berndt
Sergey Yekhanin
David P. Ward
Siena D. Ang
Patrick Garvan
Hsing-Yeh Parker
Rob Carlson
Douglas Carmean
Luis Ceze
Karin Strauss
Science Advances.
2021 August
Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis
Keisuke Motone
Nicolas Cardozo
Jeff Nivala
iScience.
Review
2021 August
Multiplexed direct detection of barcoded protein reporters on a nanopore array
Nick Cardozo
Karen Zhang
Katie Doroschak
Aerilynn Nguyen
Zoheb Siddiqui
Nicholas Bogard
Karin Strauss
Luis Ceze
Jeff Nivala
Nature Biotechnology.
2021 May
DNA Sequencing Flow Cells and the Security of the Molecular-Digital Interface
Peter Ney
Lee Organick
Jeff Nivala
Luis Ceze
Tadayoshi Kohno
Privacy Enhancing Technologies Symposium.
2021 February
Absolute and arbitrary orientation of single-molecule shapes
Ashwin Gopinath
Chris Thachuk
Anya Mitskovets
Harry A. Atwater
David Kirkpatrick
Paul W. K. Rothemund
Science.
2021 January
An empirical comparison of preservation methods for synthetic DNA data storage
Lee Organick
Bichlien Nguyen
Rachel McAmis
Weida Chen
A. Xavier Kohll
Siena Dumas Ang
Robert Grass
Luis Ceze
Karin Strauss
Small Methods.
2020 November
Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures
Kathryn Doroschak
Karen Zhang
Melissa Queen
Aishwarya Mandyam
Karin Strauss
Luis Ceze
Jeff Nivala
Nature Communications.
2020 June
PurpleDrop: A Digital Microfluidics-Based Platform for Hybrid Molecular-Electronics Applications
Ashley Stephenson
Max Willsey
Jeff McBride
Sharon Newman
Bichlien Nguyen
Christopher Takahashi
Karin Strauss
Luis Ceze
IEEE Micro.
2020 June
Quantifying molecular bias in DNA data storage
Yuan-Jyue Chen
Christopher Takahashi
Lee Organick
Callista Bee
Siena Dumas Ang
Patrick Weiss
Bill Peck
Georg Seelig
Luis Ceze
Karin Strauss
Nature Communications.
2020 June
Follow the barcoded microbes
Jeff Nivala
Science.
2020 May
Content-Based Similarity Search in Large-Scale DNA Data Storage Systems
Callista Bee
Yuan-Jyue Chen
David Ward
Xiaomeng Liu
Georg Seelig
Karin Strauss
Luis Ceze
bioRxiv.
Preprint.
2020 March
Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands
Kathryn Doroschak
Karen Zhang
Melissa Queen
Aishwarya Mandyam
Karin Strauss
Luis Ceze
Jeff Nivala
bioRxiv.
Preprint.
2020 January
Probing the physical limits of reliable DNA data retrieval
Lee Organick
Yuan-Jyue Chen
Siena Dumas Ang
Randolph Lopez
Xiaomeng Liu
Karin Strauss
Luis Ceze
Nature Communications.
2019 November
Multiplexed direct detection of barcoded protein reporters on a nanopore array
Nick Cardozo
Karen Zhang
Katie Doroschak
Aerilynn Nguyen
Zoheb Siddiqui
Karin Strauss
Luis Ceze
Jeff Nivala
bioRxiv.
Preprint.
2019 November
Scaling Microfluidics to Complex, Dynamic Protocols
Max Willsey
Ashley Stephenson
Chris Takahashi
Bichlien Nguyen
Karin Strauss
Luis Ceze
2019 IEEE/ACM International Conference on Computer-Aided Design (ICCAD).
Invited Paper
2019 September
Demonstration of End-to-End Automation of DNA Data Storage
Christopher N Takahashi
Bichlien H Nguyen
Karin Strauss
Luis H Ceze
Scientific Reports.
2019 July
DNA assembly for nanopore data storage readout
Randolph Lopez
Yuan-Jyue Chen
Siena Dumas Ang
Sergey Yekhanin
Konstantin Makarychev
Miklos Z Racz
Georg Seelig
Karin Strauss
Luis Ceze
Nature Communications.
2019 May
Molecular digital data storage using DNA
Luis Ceze
Jeff Nivala
Karin Strauss
Nature Reviews Genetics.
2019 April
High density DNA data storage library via dehydration with digital microfluidic retrieval
Sharon Newman
Ashley P Stephenson
Max Willsey
Bichlien H Nguyen
Christopher N Takahashi
Karin Strauss
Luis Ceze
Nature Communications.
2019 April
Puddle: A Dynamic, Error-Correcting, Full-Stack Microfluidics Platform
Max Willsey
Ashley P. Stephenson
Christopher N. Takahashi
Pranav Vaid
Bichlien H. Nguyen
Michal Piszczek
Christine Betts
Sharon Newman
Sarang Joshi
Karin Strauss
Luis Ceze
Proceedings of the Twenty-Third International Conference on Architectural Support for Programming Languages and Operating Systems . ASPLOS '19
2019 January
DNA Data Storage and Hybrid Molecular-Electronic Computing
Douglas Carmean
Luis Ceze
Georg Seelig
Callista Bee
Karin Strauss
Max Willsey
Proceedings of the IEEE.
2018 October
A Content-Addressable DNA Database With Learned Sequence Encodings
Callista Bee
Yuan-Jyue Chen
David Ward
Xiaomeng Liu
Georg Seelig
Karin Strauss
Luis Ceze
24th International Conference On DNA Computing and Molecular Programming (DNA24).
2018 February
Random access in large-scale DNA data storage
Lee Organick
Siena Dumas Ang
Yuan-Jyue Chen
Randolph Lopez
Sergey Yekhanin
Konstantin Makarychev
Miklos Z. Racz
Govinda Kamath
Parikshit Gopalan
Bichlien Nguyen
Christopher Takahashi
Sharon Newman
Hsing-Yeh Parker
Cyrus Rashtchian
Callista Bee
Gagan Gupta
Robert Carlson
John Mulligan
Douglas Carmean
Georg Seelig
Luis Ceze
Karin Strauss
Nature Biotechnology.
2017 November
Clustering Billions of Reads for DNA Data Storage
Cyrus Rashtchian
Konstantin Makarychev
Miklos Racz
Siena Ang
Djordje Jevdjic
Sergey Yekhanin
Luis Ceze
Karin Strauss
NIPS.
2017 August
Computer Security, Privacy, and DNA Sequencing: Compromising Computers with Synthesized DNA, Privacy Leaks, and More
Peter Ney
Karl Koscher
Lee Organick
Luis Ceze
Tadayoshi Kohno
USENIX Security.
2017 March
Scaling up DNA data storage and random access retrieval
Lee Organick
Siena Dumas Ang
Yuan-Jyue Chen
Randolph Lopez
Sergey Yekhanin
Konstantin Makarychev
Miklos Z. Racz
Govinda Kamath
Parikshit Gopalan
Bichlien Nguyen
Christopher Takahashi
Sharon Newman
Hsing-Yeh Parker
Cyrus Rashtchian
Callista Bee
Gagan Gupta
Robert Carlson
John Mulligan
Douglas Carmean
Georg Seelig
Luis Ceze
Karin Strauss
bioRxiv.
Accepted for publication at Nature Biotechnology.
2016 April
A DNA-Based Archival Storage System
James Bornholt
Randolph Lopez
Karin Strauss
Douglas M Carmean
Luis Ceze
Georg Seelig
Karin Strauss
International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS).
Selected for IEEE Micro Top Picks 2016.